Arm Yourself Against Injury
To start, simply get down on your hands and knees and lift your rib cage up toward the ceiling so you're not sagging weight down into your shoulder joints. Then lift one arm up next to your ear, which will put a little more weight onto the other arm and shoulder. When you are ready for a bigger challenge, you can progressively add to the load on the shoulder muscles by doing variations of the classic push-up. Instead of pushing up from the floor, start in a standing position facing a wall with your hands on the wall at shoulder height. As you gain strength, you can bring your body closer and closer to horizontal: First move your hands from the wall to a tabletop, then to a chair seat, and finally to the floor.
If you are starting with deconditioned shoulders, be patient; it may take several weeks or even months to work your way to the floor. You can also gradually strengthen your rotator cuff with another exercise: going from Adho Mukha Svanasana (Downward-Facing Dog Pose) to Plank Pose (the "up" position in the push-up) and back again.
These transitions can be practiced with your hands on a table, a chair seat, or the floor, depending on how strong your shoulder muscles are. This work is wonderful conditioning not only for the rotator cuff but for the triceps muscle (on the back of the upper arm) and the pectoralis major (across the chest and the front of the shoulder) as well.
In almost all yoga postures with the arms forward, as in Plank, or overhead, as in Adho Mukha Svanasana, Adho Mukha Vrksasana (Handstand), and Sirsasana, the shoulder is best stabilized with moderate external rotation. This will activate and strengthen the teres minor and infraspinatus. When you externally rotate in Plank, your elbow creases turn forward somewhat; in Sirsasana, your triceps face the same direction as your nose, not out to the side. Remember that the necessary external rotation is moderate: You are overdoing it if you feel strain in your elbows or if you can't keep the base of your thumb and index finger on the floor in Adho Mukha Svanasana or Plank.
As for the other rotator cuff muscles, the supraspinatus gets a good workout when you practice a long series of standing poses. Each time you take your arms from your sides up to shoulder height, the supraspinatus works and gets stronger. It's a little harder to be sure which yoga poses strengthen the subscapularis. For one thing, the muscle is hard to isolate; internal rotation of the shoulder is a complex movement that uses several different muscles.
For another, we simply don't internally rotate our shoulders all that often in yoga. Some of the positions in which we do internally rotate include the position of the arms in Parsvottanasana (Side Stretch Pose), that of the lower arm in Gomukhasana (Cow Face Pose), and that of the arm that wraps around the knee in Marichyasana III (Pose Dedicated to the Sage Marichi III). You also internally rotate the shoulder when you reach both arms up, interlace the fingers, and stretch the palms up toward the ceiling.